Comparison of Protein-Protein Interaction Confidence Assignment Schemes.pdf
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E. Eskin et al. (Eds.): RECOMB 2005 Ws on Regulatory Genomics, LNBI 4023, pp. 39 – 50, 2007.
? Springer-Verlag Berlin Heidelberg 2007
Comparison of Protein-Protein Interaction Confidence
Assignment Schemes
Silpa Suthram1, Tomer Shlomi2, Eytan Ruppin2, Roded Sharan2, and Trey Ideker1
1 Department of Bioengineering, University of California, San Diego, CA 92093, USA
2 School of Computer Science, Tel-Aviv University, Israel
ssuthram@
Abstract. Recent technological advances have enabled high-throughput
measurements of protein-protein interactions in the cell, producing protein
interaction networks for various species at an ever increasing pace. However,
common technologies like yeast two-hybrid can experience high rates of false
positive detection. To combat these errors, many methods have been developed
which associate confidence scores with each interaction. Here we perform the
first comparative analysis and performance assessment among these different
methods using the fact that interacting proteins have similar biological
attributes such as function, expression, and evolutionary conservation. We also
introduce a new measure, the signal to noise ratio of protein complexes
embedded in each network, to assess the quality of the different methods. We
observe that utilizing any probability scheme is always more beneficial than
assuming all observed interactions to be real. Also, schemes that assign
probabilities to individual interactions generally perform better than those
assessing the reliability of a set of interactions obtained from an experiment or a
database.
1 Introduction
Systematic elucidation of protein-protein interaction networks will be essential for
understanding how different behaviors and protein functions are integrated within the
cell. Recently, the advent of high-throughput experimental techniques like yeast two-
hybrid [1] assays and mass spectrometry [2] has lead to the discovery of large-scale
protein interaction
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